POPULATION SCALE HLA TYPING FOR HOMELAND DEFENSE

描述(申请人提供)：目前的人类白细胞抗原分型技术没有快速现场反应能力，因为它太昂贵和太复杂，不能在人口规模的紧急情况下实施。该方案的最终目标是开发一种简单、准确、低成本的方法，通过开发一种能够对大量最重要的等位基因进行群体规模分析的“人类白细胞抗原芯片”来进行复杂的人类白细胞抗原分型。美国基因组学会(GUSA)开发了一种独特的“自组装”微阵列技术和生物信息学，能够以非常低的成本大规模生产中等密度的微阵列。在这项SBIR的第一阶段，实现了以下主要目标：1)发现了原始自组装GUSA微阵列平台的使能变体，该变体允许高序列特异性和杂交信号相对于原始申请中描述的技术增加10倍。这一重大改进的观察结果是直接的、生化的、无辅助的SNP检测，具有低成本、人群规模的人类白细胞抗原配型所需的简单、准确和重复性。2)开发了生物信息学工具，以创建大量SNP选择性杂交探针，这些探针符合将探针“自组装”连接到微阵列表面所施加的物理要求；3)已证明口腔拭子是用于在HLA芯片上进行小型化HLA分型的极好的DNA来源，并开发了一种简单的方法，在现场收集口腔拭子并将其存储起来，以便在干燥状态下进行集中处理。在这项SBIR的第二阶段，人类白细胞抗原芯片开发过程将扩展到整个人类白细胞抗原基因座，并被确认为一项现场测试，以每个便携式实验室每天1000人的速度记录准确的人类白细胞抗原基因分型。贝塔测试将通过简单的外推证明，仅使用10个低成本、便携的现场实验室，就可以对大量暴露人群(每周100,000人)进行人类白细胞抗原分型。然后，这种人类白细胞抗原数据可以“实时”地用于在人类白细胞抗原水平上预测个人被生物武器感染的风险，或对同一感染源接种疫苗的个性化反应。这种低成本、便携的人类白细胞抗原芯片技术的变种可以被“衍生”用于各种其他应用：灾难中的平民身份识别或个性化药物，特别是用于自身免疫性疾病的药物。这些其他应用在技术上是相似的，但将独立开发和资助。该项目的重点是开发一种可在快速反应环境中实施的低成本人群规模的人类白细胞抗原芯片技术，以便对大量暴露人群(每周100,000人)进行快速的人类白细胞抗原分型，以确定高危个人，并在个人一级预测他们对疫苗接种的个性化反应。

DESCRIPTION (provided by applicant): Current technology for HLA typing does not have rapid field response capability because it too expensive and is too complicated to be implemented in the context of a population-scale emergency. The ultimate goal of this proposal is to develop a simple, accurate, low cost method to perform complex HLA typing through development of an "HLA Chip" which will enable population-scale analysis of a large set of the most important HLA alleles. Genomics USA (GUSA) has developed a unique "self-assembling" microarray technology and bioinformatics to enable the mass production of medium density microarrays at very low cost. In Phase I of this SBIR, the following major objectives were accomplished: 1) An enabling variant of the original self-assembling GUSA microarray platform was discovered which allows high sequence specificity and a 10-fold increase in hybridization signal relative to the technology described in the original application. The observed result of this major improvement is direct, biochemically-unaided SNP detection with the simplicity, accuracy and reproducibility required for low cost, population scale HLA typing. 2) Bioinformatics tools were developed to create large sets of SNP- selective hybridization probes that are consistent with the physical requirements imposed by "self- assembling" attachment of probes to the microarray surface and 3) It was demonstrated that a buccal swab is an excellent source of DNA for miniaturized HLA typing on the HLA Chip and a simple approach to collect buccal swabs in the field and to store them for centralized HLA processing in the dry state was also developed. In Phase II of this SBIR, the HLA Chip development process will be extended to the entire HLA locus and validated as a beta field test to document accurate HLA genotyping at a rate of 1000 individuals per day per portable laboratory site. The beta test will demonstrate, via, simple extrapolation, the ability to HLA type a large exposed population (100,000 individuals per week) using as few as 10 low cost, portable field laboratories. Such HLA data could then be used in "real time" to anticipate, at the HLA level, individual risk of infection by a biological weapon or personalized response to vaccination against the same infectious agent. Variants of this low cost, portable HLA Chip technology could be "spun off" for a variety of other applications: civilian ID in a disaster or personalized medicine, especially for autoimmune diseases. Those other applications are technically similar, but will be explored and funded independently. The project focus is the development of a low-cost population-scale HLA Chip technology that can be implemented in a rapid-response environment that would allow rapid HLA typing of a large exposed population (100,000 individuals per week) in order to identify high risk individuals and to predict, on an individual level, their personalized response to vaccination.